An improved genome assembly uncovers prolific tandem repeats in Atlantic cod

BMC Genomics

Table 1 Overview of assembly statistics

Assembly	Total size	N50	N50	Percentage	CEGMA^a	BUSCO^b	REAPR^c	FRC ^bam ^d	Potential
	assembly	contig	scaffold	gap bases					conflict
	(Mbp)	(kbp)	(Mbp)						(sequences)^e
gadMor1^f	832	2.3	0.14	26.9	444 (96.9%)	3 308 (89.4%)	2 547	4 210 772	76
ALPILM	660	4.4	0.16	28.7	424 (92.6%)	3 016 (81.6%)	19 787	2 182 096	122
NEWB454	656	6.2	1.30	24.4	435 (95.0%)	3 109 (84.1%)	18 117	2 044 008	26
CA454ILM	647	9.9	0.50	3.49	447 (97.5%)	3 379 (91.4%)	7 406	1 351 500	96
CA454PB	682	95	0.27	1.62	431 (94.1%)	3 310 (89.5%)	8 617	1 508 054	188
gadMor2^g	643	116	1.15	1.69	435 (95.0%)	3 447 (93.2%)	7 359	1 248 792	15

^aCEGMA annotates 458 highly conserved eukaryotic genes
^bBUSCO annotates 3,698 actinopterygii specific genes
^cREAPR analyses the discordance between the expected order, orientation and distance of mapped paired reads, with detected potential errors, fewer is better
^d FRC ^bam uses a similar approach as REAPR, with total number of features (i.e., potential assembly problems), fewer is better
^eNumber of sequences mapping to more than one linkage group or to multiple linkage groups, fewer is better
^fFrom [5]
^g93% of the gadMor2 assembly is additionally oriented and ordered into 23 linkage groups (Additional file 1: Table S3)

ISSN: 1471-2164